3I8V - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN PDE4A WITH 4-(3-BUTOXY-4-METHOXYPHENYL) METHYL-2-IMIDAZOLIDONE

Authors :   R. K. Y. Cheng, L. Crawley, J. Barker, M. Wood, B. Felicetti, M. Whittake

Date :   10 Jul 09 (Deposition) - 21 Jul 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.25

Chains :   Asym./Biol. Unit : A,B

Keywords :   Cyclic-Amp Specific, Camp, Hydrolase, Membrane, Phosphoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. K. Y. Cheng, L. Crawley, J. Barker, M. Wood, B. Felicetti, M. Whittaker
Crystal Structure Of Human Pde4A With 4-(3-Butoxy-4-Methoxyphenyl)Methyl-2-Imidazolidone
To Be Published
PubMed: search

Molecule 1 - CAMP-SPECIFIC 3',5'-CYCLIC PHOSPHODIESTERASE 4A
	Chains	:	A, B
	EC Number	:	3.1.4.17
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-28(A)
	Expression System Strain	:	ROSETTA
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	CATALYTIC DOMAIN
	Gene	:	PDE4A, DPDE2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	DPDE2, PDE46

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (6, 12)

No.	Name	Count	Type	Full Name
1	0MO	2	Ligand/Ion	(4R)-4-(3-BUTOXY-4-METHOXYBENZYL)IMIDAZOLIDIN-2-ONE
2	CO	1	Ligand/Ion	COBALT (II) ION
3	CSS	2	Mod. Amino Acid	S-MERCAPTOCYSTEINE
4	GOL	3	Ligand/Ion	GLYCEROL
5	MG	2	Ligand/Ion	MAGNESIUM ION
6	ZN	2	Ligand/Ion	ZINC ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HOH A:114 , HIS A:376 , HIS A:412 , ASP A:413 , ASP A:530 , HOH A:634	BINDING SITE FOR RESIDUE ZN A 2
02	AC2	SOFTWARE	HOH A:6 , HOH A:64 , HOH A:114 , HOH A:151 , HOH A:174 , ASP A:413	BINDING SITE FOR RESIDUE MG A 623
03	AC3	SOFTWARE	HOH A:105 , TYR A:371 , THR A:483 , MET A:485 , ASN A:533 , THR A:545 , ILE A:548 , PHE A:552 , MET A:569 , GLN A:581 , PHE A:584 , HOH A:634	BINDING SITE FOR RESIDUE 0MO A 1
04	AC4	SOFTWARE	HIS A:366 , ASP A:415 , PRO A:417 , HOH A:685 , HOH A:686 , HIS B:366	BINDING SITE FOR RESIDUE GOL A 3
05	AC5	SOFTWARE	ASP A:368 , HOH A:679 , HOH B:682	BINDING SITE FOR RESIDUE CO A 624
06	AC6	SOFTWARE	HOH B:74 , HIS B:376 , HIS B:412 , ASP B:413 , ASP B:530 , HOH B:636	BINDING SITE FOR RESIDUE ZN B 1
07	AC7	SOFTWARE	HOH B:38 , HOH B:60 , HOH B:69 , HOH B:74 , HOH B:162 , ASP B:413	BINDING SITE FOR RESIDUE MG B 623
08	AC8	SOFTWARE	HOH B:60 , HOH B:155 , MET B:485 , ASP B:530 , THR B:545 , ILE B:548 , MET B:549 , PHE B:552 , GLN B:581 , PHE B:584 , HOH B:636	BINDING SITE FOR RESIDUE 0MO B 2
09	AC9	SOFTWARE	GLU A:500 , ASP B:586 , HIS B:590 , ARG B:615	BINDING SITE FOR RESIDUE GOL B 624
10	BC1	SOFTWARE	HOH B:262 , THR B:390 , ASP B:603 , ILE B:607	BINDING SITE FOR RESIDUE GOL B 625

(no "SS Bond" information available for 3I8V)

Asymmetric/Biological Unit

No.	Residues
1	His A:601	-	Pro A:602
2	His B:601	-	Pro B:602

(no "SAP(SNP)/Variant" information available for 3I8V)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDEASE_I	PS00126	3'5'-cyclic nucleotide phosphodiesterases signature.	PDE4A_HUMAN	473-484	2	A:412-423 B:412-423

(no "Exon" information available for 3I8V)

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:335
 aligned with PDE4A_HUMAN | P27815 from UniProtKB/Swiss-Prot  Length:886

    Alignment length:335
                                   358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678     
          PDE4A_HUMAN   349 NSNIPRFGVKTDQEELLAQELENLNKWGLNIFCVSDYAGGRSLTCIMYMIFQERDLLKKFRIPVDTMVTYMLTLEDHYHADVAYHNSLHAADVLQSTHVLLATPALDAVFTDLEILAALFAAAIHDVDHPGVSNQFLINTNSELALMYNDESVLENHHLAVGFKLLQEDNCDIFQNLSKRQRQSLRKMVIDMVLATDMSKHMTLLADLKTMVETKKVTSSGVLLLDNYSDRIQVLRNMVHCADLSNPTKPLELYRQWTDRIMAEFFQQGDRERERGMEISPMCDKHTASVEKSQVGFIDYIVHPLWETWADLVHPDAQEILDTLEDNRDWYYSAI 683
               SCOP domains d3i8va_ A: automated matches                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhh.......hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhh...hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee.....ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------PDEASE_I    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3i8v A 288 HMNIPRFGVKTDQEELLAQELENLNKWGLNIFcVSDYAGGRSLTCIMYMIFQERDLLKKFRIPVDTMVTYMLTLEDHYHADVAYHNSLHAADVLQSTHVLLATPALDAVFTDLEILAALFAAAIHDVDHPGVSNQFLINTNSELALMYNDESVLENHHLAVGFKLLQEDNCDIFQNLSKRQRQSLRKMVIDMVLATDMSKHMTLLADLKTMVETKKVTSSGVLLLDNYSDRIQVLRNMVHCADLSNPTKPLELYRQWTDRIMAEFFQQGDRERERGMEISPMCDKHTASVEKSQVGFIDYIVHPLWETWADLVHPDAQEILDTLEDNRDWYYSAI 622
                                   297       307       317  |    327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617     
                                                          320-CSS

Chain B from PDB  Type:PROTEIN  Length:334
 aligned with PDE4A_HUMAN | P27815 from UniProtKB/Swiss-Prot  Length:886

    Alignment length:334
                                   359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679    
          PDE4A_HUMAN   350 SNIPRFGVKTDQEELLAQELENLNKWGLNIFCVSDYAGGRSLTCIMYMIFQERDLLKKFRIPVDTMVTYMLTLEDHYHADVAYHNSLHAADVLQSTHVLLATPALDAVFTDLEILAALFAAAIHDVDHPGVSNQFLINTNSELALMYNDESVLENHHLAVGFKLLQEDNCDIFQNLSKRQRQSLRKMVIDMVLATDMSKHMTLLADLKTMVETKKVTSSGVLLLDNYSDRIQVLRNMVHCADLSNPTKPLELYRQWTDRIMAEFFQQGDRERERGMEISPMCDKHTASVEKSQVGFIDYIVHPLWETWADLVHPDAQEILDTLEDNRDWYYSAI 683
               SCOP domains d3i8vb_ B: automated matches                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhh.......hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhh...hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------PDEASE_I    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3i8v B 289 MNIPRFGVKTDQEELLAQELENLNKWGLNIFcVSDYAGGRSLTCIMYMIFQERDLLKKFRIPVDTMVTYMLTLEDHYHADVAYHNSLHAADVLQSTHVLLATPALDAVFTDLEILAALFAAAIHDVDHPGVSNQFLINTNSELALMYNDESVLENHHLAVGFKLLQEDNCDIFQNLSKRQRQSLRKMVIDMVLATDMSKHMTLLADLKTMVETKKVTSSGVLLLDNYSDRIQVLRNMVHCADLSNPTKPLELYRQWTDRIMAEFFQQGDRERERGMEISPMCDKHTASVEKSQVGFIDYIVHPLWETWADLVHPDAQEILDTLEDNRDWYYSAI 622
                                   298       308       318 |     328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618    
                                                         320-CSS

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: HD-domain/PDEase-like (204)

Superfamily: HD-domain/PDEase-like (204)

Family: PDEase (118)

Protein domain: automated matches (21)

Human (Homo sapiens) [TaxId: 9606] (21)

1a	d3i8va_	A:
1b	d3i8vb_	B:

(no "CATH Domain" information available for 3I8V)

(no "Pfam Domain" information available for 3I8V)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PDE4A_HUMAN | P27815)

molecular function
	GO:0004115	3',5'-cyclic-AMP phosphodiesterase activity	Catalysis of the reaction: adenosine 3',5'-cyclic phosphate + H2O = adenosine 5'-phosphate.
	GO:0004114	3',5'-cyclic-nucleotide phosphodiesterase activity	Catalysis of the reaction: nucleoside 3',5'-cyclic phosphate + H2O = nucleoside 5'-phosphate.
	GO:0030552	cAMP binding	Interacting selectively and non-covalently with cAMP, the nucleotide cyclic AMP (adenosine 3',5'-cyclophosphate).
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008081	phosphoric diester hydrolase activity	Catalysis of the hydrolysis of a phosphodiester to give a phosphomonoester and a free hydroxyl group.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0006198	cAMP catabolic process	The chemical reactions and pathways resulting in the breakdown of the nucleotide cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate).
	GO:0035690	cellular response to drug	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
	GO:0043949	regulation of cAMP-mediated signaling	Any process which modulates the frequency, rate or extent of cAMP-mediated signaling, a series of molecular signals in which a cell uses cyclic AMP to convert an extracellular signal into a response.
	GO:0010738	regulation of protein kinase A signaling	Any process that modulates the rate, frequency, or extent of protein kinase A signaling. PKA signaling is the series of reactions, mediated by the intracellular serine/threonine kinase protein kinase A, which occurs as a result of a single trigger reaction or compound.
	GO:0007608	sensory perception of smell	The series of events required for an organism to receive an olfactory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Olfaction involves the detection of chemical composition of an organism's ambient medium by chemoreceptors. This is a neurological process.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
	GO:0042995	cell projection	A prolongation or process extending from a cell, e.g. a flagellum or axon.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0048471	perinuclear region of cytoplasm	Cytoplasm situated near, or occurring around, the nucleus.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
	GO:0032587	ruffle membrane	The portion of the plasma membrane surrounding a ruffle.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		His A:601 - Pro A:602	[ RasMol ]
		His B:601 - Pro B:602	[ RasMol ]

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	3i8v
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	PDE4A_HUMAN \| P27815
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	3.1.4.17
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	PDE4A_HUMAN \| P27815	:	2qyk 3hc8 3hdz 3tvx

(no "Related Entries Specified in the PDB File" available for 3I8V)

Description

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Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 12)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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